When you do the load, the .pdb is stripped off. The selection is 1a5m and
not 1a5m.pdb
On Thu, Apr 6, 2017 at 3:18 PM, Ahmad Abdelzaher <underoath...@gmail.com>
wrote:
> In the documentation, it said "atom selection. However i tried the
> following as you suggested:
>
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd
>
> cmd.delete('all')
> cmd.load('1a5m.pdb')
> com = cmd.centerofmass('1a5m.pdb')
> print(com)
>
> I received the following:
>
> File "C:\Users\Ahmad\Anaconda3\lib\site-packages\pymol\querying.py",
> line 1674, in centerofmass
> states = [get_selection_state(selection)]
>
> File "C:\Users\Ahmad\Anaconda3\lib\site-packages\pymol\querying.py",
> line 1641, in get_selection_state
> _self.get_object_list('(' + selection + ')')))
>
> TypeError: 'NoneType' object is not iterable
>
> On Thu, Apr 6, 2017 at 1:09 PM, David Hall <li...@cowsandmilk.net> wrote:
>
>> > how to calculate the center of mass of an entire structure
>>
>> Let's say I want the center of mas of the structure from the PDB 1vdd
>>
>> cmd.fetch('1vdd', async=0)
>>
>> cmd.centerofmass('1vdd')
>>
>> Now, I see 1vdd has a bunch of water molecules that I don't want in in my
>> calculation
>>
>> cmd.centerofmass('1vdd and not solvent')
>>
>> Now maybe I only care about chain A.
>>
>> cmd.centerofmass('1vdd and not solvent and chain A')
>>
>> I suggest reading more about selections in the pymolwiki. That is
>> actually a topic where I feel the wiki could be better organized, but
>> almost every command in pymol operates on selections, so it is a
>> fundamental concept you should spend time to understand if you are planning
>> to use pymol.
>>
>> https://pymolwiki.org/index.php/Category:Selecting
>>
>>
>> On Thu, Apr 6, 2017 at 1:13 AM, Ahmad Abdelzaher <underoath...@gmail.com>
>> wrote:
>>
>>> Hi Tsjerk,
>>>
>>> What you said makes perfect sense. Since an atom could be considered as
>>> a point with uniform density, it's center of mass is indeed its position.
>>>
>>> Which, begs the question, what is the purpose of cmd.centerofmass() and
>>> how to calculate the center of mass of an entire structure (the only
>>> calculation that would make sense with regards to the center of mass).
>>>
>>> Cheers.
>>>
>>>
>>> On Thu, Apr 6, 2017 at 6:49 AM, Tsjerk Wassenaar <tsje...@gmail.com>
>>> wrote:
>>>
>>>> Hi Ahmad,
>>>>
>>>> The center of mass of an atom is its position. A function like
>>>> cmd.centerofmass in the context of pymol only makes sense with a selection.
>>>> E.g.:
>>>>
>>>> x,y,z = cmd.centerofmass('byres n. ca')
>>>> print "COM of protein:", x, y, z
>>>>
>>>> Hope it helps,
>>>>
>>>> Tsjerk
>>>>
>>>> On Thu, Apr 6, 2017 at 6:30 AM, Ahmad Abdelzaher <
>>>> underoath...@gmail.com> wrote:
>>>>
>>>>> Well I'm assuming the selection goes in the argument of
>>>>> cmd.centerofmass(),
>>>>> however, does it have to be an atom? How should I calculate the center of
>>>>> mass for an entire protein?
>>>>>
>>>>> On Thu, Apr 6, 2017 at 4:48 AM, David Hall <li...@cowsandmilk.net>
>>>>> wrote:
>>>>>
>>>>>> It returns the x, y, and z coordinates of the center of mass as a
>>>>>> list of 3 floats, presumably in that order?
>>>>>>
>>>>>> Is there another question? The page describes the arguments and their
>>>>>> defaults so I am unsure what is lacking.
>>>>>>
>>>>>> -David
>>>>>>
>>>>>> On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher <underoath...@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> I find the documentation about the python api here to be a bit
>>>>>> lacking.
>>>>>>
>>>>>> https://pymolwiki.org/index.php/Centerofmass
>>>>>>
>>>>>> I would appreciate more info on how to use this: cmd.centerofmass()
>>>>>> returns a list of 3 floats.
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> Check out the vibrant tech community on one of the world's most
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>>>>>>
>>>>>> _______________________________________________
>>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>> Archives: http://www.mail-archive.com/py
>>>>>> mol-us...@lists.sourceforge.net
>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>>>>> t
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>
>>>>
>>>
>>
>
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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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